Project Consultation
Prior to data collection, IGB: Bioinformatics encourages researchers to meet with a staff member to discuss statistical considerations that may impact experimental design. Once data is in hand, an additional consultation is required to formulate an analysis plan and to define the scope of the work.
Data Analysis
Facility bioinformatics specialists perform data analysis based on the goals set forth during the project consultation meetings. The details of the workflow are flexible but usually involve the staff member working on the project followed by routine meetings with researchers to communicate progress and revise goals. Throughout the project, the facility staff document their work to facilitate preparation of relevant sections of publications. In addition, the facility will also handle submission of data to public repositories.
Software Support
The majority of software used by IGB: Bioinformatics is freely available but the facility does support access to proprietary software for functional analysis of gene lists generated by genomics experiments. Ingenuity Pathway Analysis can be used by working with facility staff (contact Charlie Whittaker for assistance). GeneGO MetaCore is available through MIT Libraries. In addition, some facility staff members use TIBCO Spotfire for data assembly and visualization and can arrange licenses for facility users.
Training
Training sessions covering various bioinformatics topics are offered on a regular basis and are advertised with e-mails to our community. Interested people can register for these sessions through ilabs. The cost of attendance can vary but is usually $50 per 2-3 hour session. On-demand training for individuals or small groups can also be arranged by contacting Charlie Whittaker. This customized training is billed at the same rate as bioinformatics data analysis.
Compute Cluster
The Bioinformatics Facility provides a Linux compute cluster to researchers from all sponsoring entities. Updated versions of a wide range of bioinformatics applications are installed on the cluster with version control managed using the module system and jobs are scheduled using slurm. and classroom training sessions on system usage are provided several times per year. Individual instruction is also available upon request.
Data Storage
The BCC provides a data storage resource to the KI community. Data are accessible from the facility compute cluster or via mapped network folders from computers at MIT. Off-campus access is possible using VPN. Each lab in building 76 has one TB of free space and additional TBs are billed on a monthly basis. The risk of data loss is minimized through hardware redundancy and off-site data backup.
Poster Printing
The BCC provides a poster printing service to KI labs that are located in building 76. Printing requires assistance from facility staff and at least 48 hours advanced notice.